1gdh
From Proteopedia
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CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION
Overview
D-Glycerate dehydrogenase (GDH) catalyzes the NADH-linked reduction of, hydroxypyruvate to D-glycerate. GDH is a member of a family of, NAD-dependent dehydrogenases that is characterized by a specificity for, the D-isomer of the hydroxyacid substrate. The crystal structure of the, apoenzyme form of GDH from Hyphomicrobium methylovorum has been determined, by the method of isomorphous replacement and refined at 2.4 A resolution, using a restrained least-squares method. The crystallographic R-factor is, 19.4% for all 24,553 measured reflections between 10.0 and 2.4 A, resolution. The GDH molecule is a symmetrical dimer composed of subunits, of molecular mass 38,000, and shares significant structural homology with, another NAD-dependent enzyme, formate dehydrogenase. The GDH subunit, consists of two structurally similar domains that are approximately, related to each other by 2-fold symmetry. The domains are separated by a, deep cleft that forms the putative NAD and substrate binding sites. One of, the domains has been identified as the NAD-binding domain based on its, close structural similarity to the NAD-binding domains of other, NAD-dependent dehydrogenases. The topology of the second domain is, different from that found in the various catalytic domains of other, dehydrogenases. A model of a ternary complex of GDH has been built in, which putative catalytic residues are identified based on sequence, homology between the D-isomer specific dehydrogenases. A structural, comparison between GDH and L-lactate dehydrogenase indicates a convergence, of active site residues and geometries for these two enzymes. The, reactions catalyzed are chemically equivalent but of opposing, stereospecificity. A hypothesis is presented to explain how the two, enzymes may exploit the same coenzyme stereochemistry and a similar, spatial arrangement of catalytic residues to carry out reactions that, proceed to opposite enantiomers.
About this Structure
1GDH is a Single protein structure of sequence from Hyphomicrobium methylovorum with SO4 as ligand. Active as Glycerate dehydrogenase, with EC number 1.1.1.29 Full crystallographic information is available from OCA.
Reference
Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution., Goldberg JD, Yoshida T, Brick P, J Mol Biol. 1994 Mar 4;236(4):1123-40. PMID:8120891
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